FMO DATABASE

FMODB ID: 52G5Z

Calculation Name: 2EBB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2EBB

Chain ID: A

ChEMBL ID:

UniProt ID: Q5KYG7

Base Structure: X-ray

Registration Date: 2023-06-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	96
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-766424.436149
FMO2-HF: Nuclear repulsion	726774.307754
FMO2-HF: Total energy	-39650.128395
FMO2-MP2: Total energy	-39767.709837

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:3:MET)

Summations of interaction energy for fragment #1(A:3:MET)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-12.615	-8.301	0.974	-2.003	-3.284	-0.012

Interaction energy analysis for fragmet #1(A:3:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : -0.020

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

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Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	5	LEU	0	-0.034	-0.004	2.534	-6.746	-3.527	0.956	-1.741	-2.434	-0.012
4	A	6	THR	0	-0.024	-0.048	3.830	1.474	1.749	0.000	-0.026	-0.249	0.000
5	A	7	GLU	-1	-0.918	-0.962	5.813	-0.461	-0.461	0.000	0.000	0.000	0.000
6	A	8	GLU	-1	-0.853	-0.940	9.375	-1.366	-1.366	0.000	0.000	0.000	0.000
7	A	9	GLU	-1	-0.846	-0.901	4.597	-5.946	-5.870	-0.001	-0.006	-0.068	0.000
8	A	10	VAL	0	-0.040	-0.024	8.211	0.254	0.254	0.000	0.000	0.000	0.000
9	A	11	GLN	0	-0.022	-0.008	10.372	0.223	0.223	0.000	0.000	0.000	0.000
10	A	12	ALA	0	0.018	0.020	11.926	0.134	0.134	0.000	0.000	0.000	0.000
11	A	13	LEU	0	-0.025	-0.018	8.793	0.148	0.148	0.000	0.000	0.000	0.000
12	A	14	LEU	0	-0.013	-0.022	13.067	0.160	0.160	0.000	0.000	0.000	0.000
13	A	15	GLU	-1	-0.921	-0.927	15.570	-0.547	-0.547	0.000	0.000	0.000	0.000
14	A	16	LYS	1	0.782	0.883	15.887	0.871	0.871	0.000	0.000	0.000	0.000
15	A	17	ALA	0	-0.035	-0.010	16.428	0.032	0.032	0.000	0.000	0.000	0.000
16	A	18	ASP	-1	-0.829	-0.904	18.502	-0.313	-0.313	0.000	0.000	0.000	0.000
17	A	19	GLY	0	-0.069	-0.045	21.959	0.020	0.020	0.000	0.000	0.000	0.000
18	A	20	TRP	0	-0.025	-0.015	17.270	0.042	0.042	0.000	0.000	0.000	0.000
19	A	21	LYS	1	0.880	0.932	19.551	0.291	0.291	0.000	0.000	0.000	0.000
20	A	22	LEU	0	0.045	0.038	14.021	0.030	0.030	0.000	0.000	0.000	0.000
21	A	23	ALA	0	-0.012	-0.014	17.397	0.027	0.027	0.000	0.000	0.000	0.000
22	A	24	ASP	-1	-0.839	-0.928	17.542	0.071	0.071	0.000	0.000	0.000	0.000
23	A	25	GLU	-1	-0.820	-0.894	15.420	0.166	0.166	0.000	0.000	0.000	0.000
24	A	26	ARG	1	0.773	0.878	11.857	-0.359	-0.359	0.000	0.000	0.000	0.000
25	A	27	TRP	0	0.012	0.023	12.544	0.122	0.122	0.000	0.000	0.000	0.000
26	A	28	ILE	0	0.011	0.030	12.920	-0.079	-0.079	0.000	0.000	0.000	0.000
27	A	29	VAL	0	-0.036	-0.038	15.838	0.079	0.079	0.000	0.000	0.000	0.000
28	A	30	LYS	1	0.848	0.919	19.177	0.208	0.208	0.000	0.000	0.000	0.000
29	A	31	LYS	1	0.863	0.925	21.587	0.072	0.072	0.000	0.000	0.000	0.000
30	A	32	TYR	0	0.009	-0.022	20.868	-0.009	-0.009	0.000	0.000	0.000	0.000
31	A	33	ARG	1	0.976	0.987	26.622	0.071	0.071	0.000	0.000	0.000	0.000
32	A	34	PHE	0	0.030	0.029	27.236	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	35	GLN	0	0.059	0.021	32.655	0.004	0.004	0.000	0.000	0.000	0.000
34	A	36	ASP	-1	-0.809	-0.927	35.316	-0.008	-0.008	0.000	0.000	0.000	0.000
35	A	37	TYR	0	-0.023	-0.010	33.454	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	38	LEU	0	0.051	0.020	33.513	0.004	0.004	0.000	0.000	0.000	0.000
37	A	39	GLN	0	-0.002	0.007	32.702	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	40	GLY	0	0.019	0.018	29.791	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	41	ILE	0	-0.003	-0.010	28.599	0.005	0.005	0.000	0.000	0.000	0.000
40	A	42	GLU	-1	-0.746	-0.819	28.795	0.012	0.012	0.000	0.000	0.000	0.000
41	A	43	PHE	0	-0.016	-0.015	22.595	0.004	0.004	0.000	0.000	0.000	0.000
42	A	44	VAL	0	0.012	0.000	24.316	0.002	0.002	0.000	0.000	0.000	0.000
43	A	45	ARG	1	0.851	0.899	24.134	-0.012	-0.012	0.000	0.000	0.000	0.000
44	A	46	ARG	1	0.856	0.902	24.620	0.042	0.042	0.000	0.000	0.000	0.000
45	A	47	ILE	0	0.028	0.011	19.959	0.001	0.001	0.000	0.000	0.000	0.000
46	A	48	ALA	0	-0.004	0.031	19.516	0.018	0.018	0.000	0.000	0.000	0.000
47	A	49	ALA	0	-0.004	0.004	20.108	0.029	0.029	0.000	0.000	0.000	0.000
48	A	50	ILE	0	-0.018	-0.012	16.839	0.012	0.012	0.000	0.000	0.000	0.000
49	A	51	SER	0	-0.005	-0.026	15.690	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	52	GLU	-1	-0.890	-0.919	15.592	0.366	0.366	0.000	0.000	0.000	0.000
51	A	53	ASN	0	-0.030	-0.011	16.769	0.042	0.042	0.000	0.000	0.000	0.000
52	A	54	ALA	0	-0.042	-0.018	12.443	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	55	ASN	0	-0.099	-0.039	11.958	0.121	0.121	0.000	0.000	0.000	0.000
54	A	56	HIS	0	-0.045	-0.039	8.492	0.315	0.315	0.000	0.000	0.000	0.000
55	A	57	HIS	0	-0.041	-0.040	12.422	-0.072	-0.072	0.000	0.000	0.000	0.000
56	A	58	PRO	0	-0.022	0.008	14.893	0.055	0.055	0.000	0.000	0.000	0.000
57	A	59	PHE	0	-0.010	-0.006	16.313	0.009	0.009	0.000	0.000	0.000	0.000
58	A	60	ILE	0	0.003	-0.021	19.262	-0.046	-0.046	0.000	0.000	0.000	0.000
59	A	61	SER	0	0.006	0.007	22.337	0.012	0.012	0.000	0.000	0.000	0.000
60	A	62	ILE	0	-0.018	-0.020	25.793	-0.019	-0.019	0.000	0.000	0.000	0.000
61	A	63	ASP	-1	-0.912	-0.936	28.962	0.013	0.013	0.000	0.000	0.000	0.000
62	A	64	TYR	0	0.070	0.011	31.605	-0.015	-0.015	0.000	0.000	0.000	0.000
63	A	65	LYS	1	0.857	0.923	32.710	0.024	0.024	0.000	0.000	0.000	0.000
64	A	66	LEU	0	-0.081	-0.035	28.705	-0.015	-0.015	0.000	0.000	0.000	0.000
65	A	67	ILE	0	0.039	0.030	24.593	0.013	0.013	0.000	0.000	0.000	0.000
66	A	68	THR	0	-0.044	-0.009	22.664	-0.029	-0.029	0.000	0.000	0.000	0.000
67	A	69	VAL	0	0.025	0.018	18.101	0.029	0.029	0.000	0.000	0.000	0.000
68	A	70	LYS	1	0.874	0.927	17.616	-0.118	-0.118	0.000	0.000	0.000	0.000
69	A	71	LEU	0	-0.001	0.011	12.329	0.076	0.076	0.000	0.000	0.000	0.000
70	A	72	SER	0	0.024	-0.015	10.697	-0.011	-0.011	0.000	0.000	0.000	0.000
71	A	73	SER	0	0.008	0.017	6.637	0.140	0.140	0.000	0.000	0.000	0.000
72	A	74	TRP	0	0.057	0.010	8.486	0.588	0.588	0.000	0.000	0.000	0.000
73	A	75	ARG	1	0.921	0.958	7.370	-1.621	-1.621	0.000	0.000	0.000	0.000
74	A	76	ALA	0	0.002	0.010	4.222	0.348	0.616	0.005	-0.076	-0.197	0.000
75	A	77	LYS	1	0.920	0.956	5.804	-2.654	-2.623	-0.001	-0.001	-0.028	0.000
76	A	78	GLY	0	0.031	0.009	8.505	-0.427	-0.427	0.000	0.000	0.000	0.000
77	A	79	LEU	0	0.022	0.039	8.073	0.382	0.382	0.000	0.000	0.000	0.000
78	A	80	THR	0	0.009	-0.015	3.453	-1.049	-0.604	0.015	-0.153	-0.308	0.000
79	A	81	LYS	1	0.876	0.910	4.979	1.708	1.708	0.000	0.000	0.000	0.000
80	A	82	LEU	0	0.067	0.034	6.042	0.317	0.317	0.000	0.000	0.000	0.000
81	A	83	ASP	-1	-0.722	-0.832	7.875	0.389	0.389	0.000	0.000	0.000	0.000
82	A	84	PHE	0	0.039	-0.003	9.578	0.097	0.097	0.000	0.000	0.000	0.000
83	A	85	ASP	-1	-0.839	-0.897	10.213	-0.979	-0.979	0.000	0.000	0.000	0.000
84	A	86	LEU	0	0.027	0.006	11.339	0.089	0.089	0.000	0.000	0.000	0.000
85	A	87	ALA	0	-0.001	0.006	13.735	0.046	0.046	0.000	0.000	0.000	0.000
86	A	88	LYS	1	0.976	0.981	15.425	0.641	0.641	0.000	0.000	0.000	0.000
87	A	89	GLN	0	0.010	0.009	14.617	0.017	0.017	0.000	0.000	0.000	0.000
88	A	90	TYR	0	0.000	-0.030	15.869	0.030	0.030	0.000	0.000	0.000	0.000
89	A	91	ASP	-1	-0.794	-0.860	19.662	-0.241	-0.241	0.000	0.000	0.000	0.000
90	A	92	GLU	-1	-0.880	-0.923	21.105	-0.184	-0.184	0.000	0.000	0.000	0.000
91	A	93	VAL	0	-0.018	-0.009	22.125	0.022	0.022	0.000	0.000	0.000	0.000
92	A	94	TYR	0	-0.047	-0.044	24.092	0.006	0.006	0.000	0.000	0.000	0.000
93	A	95	ASN	0	-0.018	-0.024	24.890	0.022	0.022	0.000	0.000	0.000	0.000
94	A	96	GLN	0	-0.048	-0.014	26.797	0.019	0.019	0.000	0.000	0.000	0.000
95	A	97	MET	0	-0.096	-0.032	28.542	0.011	0.011	0.000	0.000	0.000	0.000
96	A	98	LYS	1	0.858	0.951	28.243	0.153	0.153	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:MET)